Variant 1-200553493-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014875.3(KIF14):c.4842C>T(p.Asp1614=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0034 in 1,613,888 control chromosomes in the GnomAD database, including 115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 12 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 103 hom. )

Consequence

KIF14
NM_014875.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0910

Variant links:

Genes affected

KIF14 (HGNC:19181): (kinesin family member 14) This gene encodes a member of the kinesin-3 superfamily of microtubule motor proteins. These proteins are involved in numerous processes including vesicle transport, chromosome segregation, mitotic spindle formation, and cytokinesis. In human HeLa-S3 and 293T cells, this protein is localized to the cytoplasm during interphase, to the spindle poles and spindle microtubules during mitosis, and to the midbody during cytokinesis. An internal motor domain displays microtubule-dependent ATPase activity, consistent with its function as a microtubule motor protein. Knockdown of this gene results in failed cytokinesis with endoreplication, which results in multinucleated cells. This gene has been identified as a likely oncogene in breast, lung and ovarian cancers, as well as retinoblastomas and gliomas. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]

KIF14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-200553493-G-A is Benign according to our data. Variant chr1-200553493-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 721215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.091 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF14	NM_014875.3 linkuse as main transcript	c.4842C>T	p.Asp1614=	synonymous_variant	30/30	ENST00000367350.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF14	ENST00000367350.5 linkuse as main transcript	c.4842C>T	p.Asp1614=	synonymous_variant	30/30	2	NM_014875.3	P1
KIF14	ENST00000614960.4 linkuse as main transcript	c.4842C>T	p.Asp1614=	synonymous_variant	29/29	1		P1

Frequencies

GnomAD3 genomes

AF:

0.00379

AC:

575

AN:

151886

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000459

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0600

Gnomad SAS

AF:

0.00726

Gnomad FIN

AF:

0.0137

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000971

Gnomad OTH

AF:

0.00240

GnomAD3 exomes

AF:

0.00648

AC:

1630

AN:

251402

Hom.:

AF XY:

0.00617

AC XY:

838

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.000595

Gnomad EAS exome

AF:

0.0568

Gnomad SAS exome

AF:

0.00255

Gnomad FIN exome

AF:

0.0136

Gnomad NFE exome

AF:

0.00118

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00336

AC:

4909

AN:

1461884

Hom.:

103

Cov.:

AF XY:

0.00343

AC XY:

2497

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.000984

Gnomad4 ASJ exome

AF:

0.000650

Gnomad4 EAS exome

AF:

0.0698

Gnomad4 SAS exome

AF:

0.00318

Gnomad4 FIN exome

AF:

0.0138

Gnomad4 NFE exome

AF:

0.000737

Gnomad4 OTH exome

AF:

0.00379

GnomAD4 genome

AF:

0.00379

AC:

576

AN:

152004

Hom.:

Cov.:

AF XY:

0.00483

AC XY:

359

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.000169

Gnomad4 AMR

AF:

0.000459

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.0604

Gnomad4 SAS

AF:

0.00727

Gnomad4 FIN

AF:

0.0137

Gnomad4 NFE

AF:

0.000971

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00114

Hom.:

Bravo

AF:

0.00298

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.000491

EpiControl

AF:

0.00107

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 09, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -

Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome;C4693572:Microcephaly 20, primary, autosomal recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 29, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.3

DANN

Benign

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over